Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (17)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Tsai, J.
Right arrow Articles by Gerstein, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tsai, J.
Right arrow Articles by Gerstein, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 18 no. 7 2002
Pages 985-995
© 2002 Oxford University Press

Calculations of protein volumes: sensitivity analysis and parameter database

Jerry Tsai 1,* and Mark Gerstein 2

1 Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
2 Department of Molecular Biophysics and Biochemistry, Yale University, Bass Center, 266 Whitney Avenue, P.O. Box 208114, New Haven, CT 06520-8114, USA

Received on October 30, 2001 ; revised on May 23, 2001 and October 14, 2001 ; accepted on December 11, 2001

Motivation: The precise sizes of protein atoms in terms of occupied packing volume are of great importance. We have previously presented standard volumes for protein residues based on calculations with Voronoi-like polyhedra. To understand the applicability and limitations of our set, we investigated, in detail, the sensitivity of the volume calculations to a number of factors: (i) the van der Waals radii set, (ii) the criteria for including buried atoms in the calculations or atom selection, (iii) the method of positioning the dividing plane in polyhedra construction, and (iv) the set of structures used in the averaging.

Results: We find that different radii sets have only moderate affects to the distribution and mean of volumes. Atom selection and dividing plane methods cause larger changes in protein atoms volumes. More significantly, we show how the variation in volumes appears to be clearly related to the quality of the structures analyzed, with higher quality structures giving consistently smaller average volumes with less variance.

Availability/Supplementary Information: Programs and associated data files are available from http://bioinfo.mbb.yale.edu/geometry and http://molmovdb.org. In particular, we make available an extensive database of many different sets of protein geometric parameters.

Contact: JerryTsai{at}TAMU.edu; Mark.Gerstein{at}Yale.edu

* To whom correspondence should be addressed.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Cell Sci.Home page
R. G. Parton, M. Hanzal-Bayer, and J. F. Hancock
Biogenesis of caveolae: a structural model for caveolin-induced domain formation.
J. Cell Sci., March 1, 2006; 119(Pt 5): 787 - 796.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
H. Edelsbrunner and P. Koehl
The weighted-volume derivative of a space-filling diagram
PNAS, March 4, 2003; 100(5): 2203 - 2208.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.